CompaRNA - on-line benchmarks of RNA structure prediction methods

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Metric	RNAalifold(seed)		Mastr(20)
MCC	0.578	>	0.394
Average MCC ± 95% Confidence Intervals	0.578 ± 0.058	>	0.386 ± 0.184
Sensitivity	0.364	>	0.207
Positive Predictive Value	0.919	>	0.754
Total TP	227	>	129
Total TN	149667	<	149743
Total FP	28	<	45
Total FP CONTRA	7	>	3
Total FP INCONS	13	<	39
Total FP COMP	8	>	3
Total FN	396	<	494
P-value	2.34821445183e-08

Comparison of performance of RNAalifold(seed) and Mastr(20). Positive Predictive Value (PPV) is plotted against sensitivity. Each dot represents a single test of each method. See tables below for raw data (individual counts for RNAalifold(seed) and Mastr(20)).
Average Matthews Correlation Coefficients (MCC) with 95% confidence intervals (CIs) were plotted for different RNA families, for which at least 3 members were present in the benchmarking dataset. 'n' denotes the number of MCCs used to calculate the average and CI. See tables below for raw data (individual counts for RNAalifold(seed) and Mastr(20)).
Comparison of average Matthews Correlation Coefficients (MCCs) for RNAalifold(seed) and Mastr(20). The whiskers correspond to 95% confidence intervals (CIs). 'n' denotes the number of MCCs used to calculate average MCCs and CIs. See tables below for raw data (individual counts for RNAalifold(seed) and Mastr(20)).

Total Scores
MCC	0.578
Average MCC ± 95% Confidence Intervals	0.578 ± 0.058
Sensitivity	0.364
Positive Predictive Value	0.919
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.52	0.27	1.00	3	403	0	0	0	0	8
3GX2_A	SAM links to Rfam database...	0.74	0.55	1.00	22	4349	1	0	0	1	18
3IVN_B	Purine links to Rfam database...	0.61	0.48	0.79	15	2327	4	2	2	0	16
3IZ4_A	tmRNA links to Rfam database...	0.42	0.21	0.85	28	70843	5	1	4	0	104
3JYX_4	5_8S_rRNA links to Rfam database...	0.46	0.21	1.00	7	12239	2	0	0	2	26
3LA5_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2466	3	1	2	0	18
3NPB_A	SAM links to Rfam database...	0.66	0.48	0.92	22	6997	3	1	1	1	24
3O58_3	5_8S_rRNA links to Rfam database...	0.51	0.26	1.00	9	12394	0	0	0	0	26
3PDR_A	ykoK links to Rfam database...	0.68	0.46	1.00	33	12847	1	0	0	1	39
3RKF_A	Purine links to Rfam database...	0.63	0.47	0.84	16	2192	3	1	2	0	18
3SD1_A	THF links to Rfam database...	0.58	0.40	0.85	17	3896	3	1	2	0	25
4A1C_2	5_8S_rRNA links to Rfam database...	0.39	0.15	1.00	5	11776	2	0	0	2	28
4AOB_A	SAM links to Rfam database...	0.72	0.52	1.00	22	4349	1	0	0	1	20
4ENB_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1269	0	0	0	0	13
4ENC_A	crcB links to Rfam database...	0.56	0.32	1.00	6	1320	0	0	0	0	13

Total Scores
MCC	0.394
Average MCC ± 95% Confidence Intervals	0.386 ± 0.184
Sensitivity	0.207
Positive Predictive Value	0.754
Nr of predictions	15

RNA Chain	Rfam family	MCC	SENS	PPV	TP	TN	FP	FP CONTRA	FP INCONS	FP COMP	FN
2KDQ_B	mir-TAR links to Rfam database...	0.95	0.91	1.00	10	396	0	0	0	0	1
3GX2_A	SAM links to Rfam database...	0.39	0.28	0.55	11	4351	10	0	9	1	29
3IVN_B	Purine links to Rfam database...	0.78	0.65	0.95	20	2325	1	1	0	0	11
3IZ4_A	tmRNA links to Rfam database...	0.00	0.00	0.00	0	70876	0	0	0	0	132
3JYX_4	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12246	0	0	0	0	33
3LA5_A	Purine links to Rfam database...	0.76	0.59	1.00	20	2465	0	0	0	0	14
3NPB_A	SAM links to Rfam database...	0.30	0.24	0.39	11	6993	18	1	16	1	35
3O58_3	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	12403	0	0	0	0	35
3PDR_A	ykoK links to Rfam database...	0.00	0.00	0.00	0	12880	0	0	0	0	72
3RKF_A	Purine links to Rfam database...	0.70	0.50	1.00	17	2194	0	0	0	0	17
3SD1_A	THF links to Rfam database...	0.61	0.50	0.75	21	3888	7	1	6	0	21
4A1C_2	5_8S_rRNA links to Rfam database...	0.00	0.00	0.00	0	11781	0	0	0	0	33
4AOB_A	SAM links to Rfam database...	0.39	0.26	0.58	11	4352	9	0	8	1	31
4ENB_A	crcB links to Rfam database...	0.39	0.16	1.00	3	1272	0	0	0	0	16
4ENC_A	crcB links to Rfam database...	0.51	0.26	1.00	5	1321	0	0	0	0	14

Matthews Correlation Coeffient, Sensitivity and Positive Predictive Value have been calculated based on the paper by Gardener & Giegerich, 2004.